It's unintentionally funny, since the scene is anything but funny, but Mink coldly wondering why Aoba cares so much about his AllMate since they're just goods, when his own AllMate is greatly decorated in a manner that could only be done by him, counts as quite the Hypocritical Humor.
There's a scene early on in the game were Noiz breaks into Aoba's room, and as they're arguing, Koujaku ends up with them too, and Clear joins as well by rising up from the bottom of Aoba's window and basically breaking in. This almost seems like it could've been a serious scene, but then Granny breaks up the fight, and they all end up in the kitchen discussing their dispute over donuts. And Let's not forget Clear's "MAAAAAAA-SUUUUUU-TAAAAAA!"
When all the main characters discuss about where Tae is, Clear says that he knows the area since he used to take walks around there. Normally, due to his usual behavior, none of them believe him. Clear notices this and is clearly dismayed, and draws a map of said area — which looks like a child's scribble. However, when Noiz confirms it to be actually accurate, Clear is all the more irritated that they didn't believe him.
Near the end of Noiz's route, it turns out that Mio, of the three bratty kids, has developed a crush on Noiz. The way she shows this is by handing him a love letter written in crayon, and then angrily saying that he didn't have to read it. Both Noiz and Aoba are clearly at a loss.
Another Clear moment: He calls Aoba at Platinum Jail, having found a secret entrance to Oval Tower. Aoba follows a map provided... only to find it was actually a place named "Overr Tower".
And yet another one with Clear, when he tried to make Aoba feel better by preparing him food... while wearing nothing but an apron (and his gas mask).
In RE:Code, he's not completely naked and wears a pair of boxers, but the scene remains just as hilarious.
During a walk in the Green Playground, Noiz purchases various types of food, not knowing what they are. When Aoba asks what he's been eating, Noiz nonchalantly replies he's been living off delivery pizza and pasta for the last few years.
The second Aoba looks away, Noiz steals one of his takoyaki with the most serious face in history.
The event that causes him to act so is often a funny moment, too.
Aoba punishing Clear for making him look at a mirror while they were having sex, by pinching his nose. The noise Clear makes when he does so is hilarious.
The entire scene of Aoba and Koujaku arguing about the latter keeping the cut pieces of the former's hair, since Aoba finds it creepy. When Koujaku tries to argue how important his hair is to him, both of them become more and more embarrassed till they end up saying nothing, with their faces beet red.
Aoba's constant irritation of Ren being taller than him in Rhyme and in real life as Sei despite Sei only being 1 cm taller!
Aoba imitating one of Koujaku's many fangirls in the drama CD.
"I failed to be the 'top'.", said by Aoba in Ren's route.
In the drama CD, Clear saw an announcement that dictates the top ten things women expect from their lovers. Then later, when visiting Aoba during the latter's worktime, he acts completely out of character by acting manly and suave, then when exiting the shop in said manner, accidentally hits his face against the door. Needless to say, Aoba is left dumbfounded.
In the following track, Aoba suggests that Clear tries to call him by his name without using any honorifics. Clear is completely embarrassed by the thought, panicking that he would explode just from trying to do it. Then he mutters that he feels like he is in "a dream within a dream within a dream".
Equally funny and heartwarming: in the drama CD, Aoba prepares a special dinner for Mink. Mink notices this, and Aoba makes him guess why. Before he could even give a hint, Mink immediately gives the correct answer: it's the anniversary of a year passing since Aoba's arrival. Aoba is disappointed that he guessed it right so quickly, but then points out that he could only answer right away if he remembered it too, with Mink immediately changing the topic by reminding Aoba that the food will get cold.
The April Fools drama features Noiz modifying Ren's voice that he sounds a lot more high-pitched than his default deep voice, taking his usual Vocal DissonanceUp to Eleven. Both Ren and Aoba are promptly freaked out and disturbed, that Aoba immediately begs Noiz to change Ren's voice back to his normal one.